GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB

Model Identifier
BIOMD0000000893
Short description
This is a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation.
Format
SBML
(L2V4)
Related Publication
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On the effect of circadian oscillations on biochemical cell signaling by NF-κB.
- González-Miranda JM
- Journal of theoretical biology , 10/ 2013 , Volume 335 , pages: 283-294 , PubMed ID: 23820037
- Departamento de Física Fundamental, Universidad de Barcelona, Av. Diagonal 647, 08028 Barcelona, Spain. jmgonzalezm@ub.edu
- We report the results of a numerical investigation of a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation. The main result is that a circadian rhythm, even when it represents a weak perturbation, enhances the signaling capabilities of NF-κB oscillations. This is done by turning rest states into periodic oscillations, and periodic oscillations into quasiperiodic oscillations. Strong perturbations result in complex periodic oscillations and even in chaos. Circadian rhythms would then result in a NF-κB dynamics that is more complex than the simple oscillations and rest states, initially reported for this model. This renders it more amenable for information coding.
Contributors
Submitter of the first revision: Johannes Meyer
Submitter of this revision: Rahuman Sheriff
Modellers: Rahuman Sheriff, Johannes Meyer
Submitter of this revision: Rahuman Sheriff
Modellers: Rahuman Sheriff, Johannes Meyer
Metadata information
is (2 statements)
isDescribedBy (1 statement)
isDerivedFrom (1 statement)
hasProperty (4 statements)
isDescribedBy (1 statement)
isDerivedFrom (1 statement)
hasProperty (4 statements)
Mathematical Modelling Ontology
Ordinary differential equation model
NCIt Biological Rhythm
Experimental Factor Ontology circadian rhythm
NCIt Signaling Pathway
NCIt Biological Rhythm
Experimental Factor Ontology circadian rhythm
NCIt Signaling Pathway
Curation status
Curated
Tags
Connected external resources
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Model files |
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GonzalezMiranda2013.xml | SBML L2V4 Representation of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB | 28.71 KB | Preview | Download |
Additional files |
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GonzalezMiranda2013.cps | COPASI file of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB | 52.03 KB | Preview | Download |
GonzalezMiranda2013.sedml | SED-ML file of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB | 1.70 KB | Preview | Download |
- Model originally submitted by : Johannes Meyer
- Submitted: Dec 16, 2019 10:11:37 AM
- Last Modified: Oct 8, 2021 8:03:49 AM
Revisions
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Version: 5
- Submitted on: Oct 8, 2021 8:03:49 AM
- Submitted by: Rahuman Sheriff
- With comment: Automatically added model identifier BIOMD0000000893
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Version: 3
- Submitted on: Dec 16, 2019 10:11:37 AM
- Submitted by: Johannes Meyer
- With comment: Automatically added model identifier BIOMD0000000893
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Legends
: Variable used inside SBML models
: Variable used inside SBML models
Species
Reactions
Reactions | Rate | Parameters |
---|---|---|
z => ; x | compartment*C*z*(1-x)/(epsilon+z) | epsilon = 2.0E-5; C = 0.035 |
y => | compartment*k1*y | k1=1.0 |
=> z; y | compartment*y | [] |
=> y; x | compartment*x*x | [] |
x => ; z | compartment*B*z*x/(delta+x) | delta = 0.029; B = 954.5 |
=> x; z | compartment*A*(1-x)/(epsilon+z) | A = 0.007; epsilon = 2.0E-5 |
Curator's comment:
(added: 16 Dec 2019, 10:11:27, updated: 16 Dec 2019, 10:11:27)
(added: 16 Dec 2019, 10:11:27, updated: 16 Dec 2019, 10:11:27)
Reproduced plot of Figure 4(b) in the original publication.
Model simulated and plot produced using COPASI 4.24 (Build 197).